It had its origin in the strain on communications within the Imperium caused by the long lag times dictated by the very size of the Imperium.

To cite one cause, however, would be simplistic. The diverse backgrounds of the many constituents of the Imperium had its effects, as did rivalry for power by major naval and military commanders, and a lessening in the Imperium's expansionist tendencies.

The spark which started the Civil War was thrown off by the First Frontier War (589 to 604) in the Spinward Marches. Communications lags and a lack of preparedness forced the Marches to conduct most of the war on its own, with little additional help or support from the Imperium.

Grand Admiral of the Marches Olav hault-Plankwell forced the war to an end, he found solid support for a new government. Marching on the Capital with his war fleet, he forced an audience with Empress Jaqueline I, supposedly for recognition of his war effort. In the course of the meeting in 606, he personally murdered the Empress, then proclaiming himself Emperor by right of fleet control. The ensuing power struggle lasted through eighteen years and eighteen emperors.

The fighting in the Civil War was of two varieties: fringe battles for power bases, and central battles for power in the Core. The fringe battles were fought throughout the Imperium as rival factions recruited forces. Once any power block built up enough strength to make a victory seem possible, the forces were moved to the Core and used to either seize power or to wrest it away from someone else. But there was also a cheaper, easier route open to many.

The dynastic crisis of 244 had produced a precedent for the assassination of the emperor if he or she overstepped the bounds of legitimate activity. The concept was introduced to legitimize the elimination of Cleon the Mad and never intended for any other purpose. Nevertheless, in the turmoil of the Civil War, assassination was introduced and accepted, at least by those utilizing the technique, as a way of promoting a succession in government.

The line of Emperors during the Civil War came mostly from naval officers, and they are collectively called the Emperors of the Flag. Of these eighteen, seven were assassinated, ten were killed in battle, and one survived — Arbellatra.

During the course of the Civil War, the Outworld Coalition (of Zhodani and Vargr) saw that their defeat in the First Frontier War at the hands of Olav need not be permanent. They attacked again in the Second Frontier War (615 to 620). Their defeat in that war had greater effects than they would know. Grand Admiral Arbellatra managed the meager forces of the Imperium against the Coalition and managed to force a second defeat.

Arbellatra's strategy after the war was (like Olav) to march on the Capital and seize power. She, however, did not make the mistake of seizing the throne. Instead, she defeated the putative emperor and then took possession of power, holding it in trust for a rightful successor. She held the post of regent for seven years while a search for a member of Jaqueline's family could be found to take the throne. In the stability that followed with her as regent, she made an impression on the Moot and succeeded in establishing a broad power base. Ultimately, the Moot approached her to take the throne herself, an end which was probably in her mind all along.

With the end of the two Frontier Wars and the Civil War, the Imperium entered a period of renewed expansions and consolidation. The express boat system was established to enhance government, commercial, and private communications; the Solomani influence in the Imperium was lessened and replaced with a more cosmopolitan policy; renewed efforts at interior development of existing Imperial territories provided a new focus for the nobles of the Moot.